Hi all,
I would like to compare the abundance of my gene(s) of interest across many published metagenomes. Typically we would normalize the number of hits to the gene length and number of sequences (or mbp) to get relative abundances, and perhaps also normalize to the abundance of single-copy core genes to get an estimate of the gene number per genome equivalents. This has been done many times, but to the best of my knowledge all such comparison were between metagenomes sequenced using the same technology (e.g. within the GOS dataset, which is all Sanger).
My question is, can this approach be extended to compare across metagenomes produced with different sequencing technologies (e.g. compare the relative abundance in a marine metagenome sequenced with Sanger to human gut sample sequenced with Illumina)? Are such comparisons valid between samples with very different sequencing coverage? There must be some intelligent controls one would have to run... any suggestions welcome! Also, if anyone is aware of publications where such comparisons have been performed I would love to hear about them!
Thanks
Daniel
I would like to compare the abundance of my gene(s) of interest across many published metagenomes. Typically we would normalize the number of hits to the gene length and number of sequences (or mbp) to get relative abundances, and perhaps also normalize to the abundance of single-copy core genes to get an estimate of the gene number per genome equivalents. This has been done many times, but to the best of my knowledge all such comparison were between metagenomes sequenced using the same technology (e.g. within the GOS dataset, which is all Sanger).
My question is, can this approach be extended to compare across metagenomes produced with different sequencing technologies (e.g. compare the relative abundance in a marine metagenome sequenced with Sanger to human gut sample sequenced with Illumina)? Are such comparisons valid between samples with very different sequencing coverage? There must be some intelligent controls one would have to run... any suggestions welcome! Also, if anyone is aware of publications where such comparisons have been performed I would love to hear about them!
Thanks
Daniel
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